DreINT0109556 @ danRer10
Intron Retention
Gene
ENSDARG00000021140 | pabpc1b
Description
poly A binding protein, cytoplasmic 1 b [Source:ZFIN;Acc:ZDB-GENE-050308-1]
Coordinates
chr19:12218880-12219309:-
Coord C1 exon
chr19:12219116-12219309
Coord A exon
chr19:12218996-12219115
Coord C2 exon
chr19:12218880-12218995
Length
120 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
GCCTGATATCCTTTCTTAAGGTG
3' ss Score
7.18
Exon sequences
Seq C1 exon
CTGAACGGGCTCTAGACACAATGAACTTTGATGTCATCAAAGGTAGACCTGTCCGCATTATGTGGTCTCAGCGTGACCCTTCTCTGAGGAAGAGCGGCGTCGGAAACATCTTCATTAAAAATCTGGATAAGTCTATTGACAACAAAGCTCTTTATGACACCTTCTCAGCGTTTGGCAACATCTTGTCATGCAAG
Seq A exon
GTAAGCCGCATACACAAGGTATTTCGCTGAGTTTTGATGATTACGAATGTTGTAATTTGTGCATGTGTGTTTCTGTTAGTCAGTGTGTGCATGATTTTCTGCCTGATATCCTTTCTTAAG
Seq C2 exon
GTGGTTTGTGACGAGAATGGCTCAAAGGGCTACGGCTTTGTGCACTTTGAGACCCAGGAGGCTGCTGAAAGAGCCATTGAGAAAATGAACGGCATGTTGCTGAATGACAGAAAAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021140:ENSDART00000032474:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(25.4=27.7),PF0007617=RRM_1=PU(40.6=43.1)
A:
NA
C2:
PF0007617=RRM_1=FE(55.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCATTATGTGGTCTCAGCGT
R:
TGTCATTCAGCAACATGCCGT
Band lengths:
250-370
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]